New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	4960665 =	39 (0.700)	3 (0.060)	3/242	NT	7.2%	coding (154/333 nt)	fliE	flagellar hook‑basal body complex protein FliE
	?	NC_002947	4960707 =	40 (0.760)					coding (112/333 nt)	fliE	flagellar hook‑basal body complex protein FliE

ACGCTGGCCTTTTGCGAAGCGATCATCACGTCAGTCAGGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGACGATTGAATTCAACACCTTGGCTCATGACCCTTCTCTCTCCTGCGGCCGCATTTTTTT  >  NC_002947/4960562‑4960850                                                                                                                                                  |                                                                                                                                                acGCTGGCCTTTTGCGAAGCGATCATCACGTCAGTCAGGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTg                                                                                                                                              >  2:202515/1‑149 (MQ=255)  gtgttgaattcaatcgtctgatgttggacatgcgggccatgcaggccgatgccatgtcgctgcccaaggtaactgccgcccccgagctggcgccagggcaaaGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGc                                                                                                                                             >  6:312154‑M1/103‑149 (MQ=255)   gCTGGCCTTTTGCGAAGCGATCATCACGTCAGTCAGGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGcc                                                                                                                                            >  7:30099/1‑149 (MQ=255)    cTGGCCTTTTGCGAAGCGATCATCACGTCAGTCAGGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGccc                                                                                                                                           <  4:267619/149‑1 (MQ=255)       gCCTTTTGCGAAGCGATCATCACGTCAGTCAGGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCt                                                                                                                                          <  7:256517/147‑1 (MQ=255)              gCGAAGCGATCATCACGTCAGTCAGGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAg                                                                                                                                  >  4:33456/1‑148 (MQ=255)               cGAAGCGATCATCACGTCAGTCAGGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGAGAAGGTGCTTTGCCCTGGCTCCAGCt                                                                                                                                >  7:261120/1‑149 (MQ=255)                     gATCATCACGTCAGTCAGGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGACTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCggggg                                                                                                                          >  2:261375/1‑149 (MQ=255)                              gtcagtcaGGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGtt                                                                                                                  >  4:100330/1‑148 (MQ=255)                                  gtcagGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCtt                                                                                                             <  6:202752/149‑1 (MQ=255)                                   tcagGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCggggg                                                                                                                          <  3:121435/135‑1 (MQ=255)                                   tcagGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCggggg                                                                                                                          >  4:121435/1‑135 (MQ=255)                                   gcagGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTg                                                                                                            <  3:100330/148‑1 (MQ=255)                                       gTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTggg                                                                                                          >  5:224689/1‑147 (MQ=255)                                           aCGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGa                                                                                                    <  5:307102/149‑1 (MQ=255)                                            cgccgcTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGAc                                                                                                   <  8:30099/149‑1 (MQ=255)                                               cgcTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATg                                                                                                >  8:207511/1‑149 (MQ=255)                                               cgcTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGCGGCGGCAGTTACCTTGGGCAGCGACATg                                                                                                <  1:202515/149‑1 (MQ=255)                                                    ttGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATc                                                                                           >  2:108608/1‑149 (MQ=255)                                                      gCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCAt                                                                                            <  3:33456/146‑1 (MQ=255)                                                      gCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCgg                                                                                         >  3:131758/1‑149 (MQ=255)                                                        cGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGc                                                                                        >  8:159181/1‑148 (MQ=255)                                                        cGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGc                                                                                        <  7:159181/148‑1 (MQ=255)                                                               gAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATgg                                                                                <  3:310588/149‑1 (MQ=255)                                                               gAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATg                                                                                 <  1:108608/148‑1 (MQ=255)                                                                                  gTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAg                                                             <  7:207511/149‑1 (MQ=255)                                                                                   tCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGa                                                            >  8:316939/1‑149 (MQ=255)                                                                                      agtcTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCACTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGACGa                                                         >  8:194456/4‑149 (MQ=255)                                                                                      aGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCt                                                                                      >  8:153756/1‑120 (MQ=255)                                                                                      aGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCt                                                                                      <  7:153756/120‑1 (MQ=255)                                                                                        gCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGACGAtt                                                       <  7:316939/149‑1 (MQ=255)                                                                                          ttGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGAc                                                           >  3:267322/1‑143 (MQ=255)                                                                                          ttGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGAc                                                           <  4:267322/143‑1 (MQ=255)                                                                                             ctgcGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCATTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGACGATTGAAtt                                                  >  2:207415/1‑149 (MQ=255)                                                                                                   gcaaagcaccttcgccgacatgctcggccaggccatcggcaaggtgcTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGACGATTGAATTCAacac                                            >  6:312154‑M2/48‑149 (MQ=255)                                                                                                      aTGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCATACGATTGAATTCAACACCtt                                         >  2:265267/1‑149 (MQ=255)                                                                                                      aTGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGACGATTGAATTCAACACCtt                                         <  6:224689/149‑1 (MQ=255)                                                                                                        GCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGACGATTGAATTCAACACCTTgg                                       <  6:345692‑M1/149‑1 (MQ=255)                                                                                                            cttcgccgacatgctcggccaggccatcggcaaggtgcTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTggg                                                                                                          >  3:14780‑M2/39‑78 (MQ=255)                                                                                                            cttcgccgacatgctcggccaggccatcggcaaggtgcTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTggg                                                                                                          <  4:14780‑M2/40‑1 (MQ=255)                                                                                                            CTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGACGATTGAATTCAACACCTTGGCTCa                                   <  4:188552‑M1/149‑1 (MQ=255)                                                                                                            CTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGACGATTGAATTCAACACCTTGGCTCa                                   <  3:212703‑M1/149‑1 (MQ=255)                                                                                                            CTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGACGATTGAATTCAACACCTTGGCTCa                                   >  5:345692‑M1/1‑149 (MQ=255)                                                                                                                      gcctggccGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGACGATTGAATTCAACACCTTGGCTCATGACCCTtct                         >  6:346361/1‑149 (MQ=255)                                                                                                                      gcctggccGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGACGATTGAATTCAACACCTTGGCTCATGACCCTtct                         <  5:346361/149‑1 (MQ=255)                                                                                                                       cctggccGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGACGATTGAATTCAACACCt                                          <  6:202805/131‑1 (MQ=255)                                                                                                                       cctggccGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGACGATTGAATTCAACACCt                                          >  5:202805/1‑131 (MQ=255)                                                                                                                       cctggccGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGACGATTGAATTCAACACCTTGGCTCATGACCCTtctc                        >  8:216291/1‑149 (MQ=255)                                                                                                                        ctggccGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGACGATTGAATTCAACACCTTGGCTCATGACCCTtctct                       <  7:194456/149‑1 (MQ=255)                                                                                                                                             ggtgcTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGACGATTGAATTCAACACCTTGGCTCATGACCCTTCTCTCTCCTGCGGCCGCAttttttt  <  7:216291‑M2/144‑1 (MQ=255)                                                                                                                                             ggtgcTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGACGATTGAATTCAACACCTTGGCTCATGACCCTTCTCTCTCCTGCGGCCGCAttttttt  <  4:212703‑M2/144‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                ACGCTGGCCTTTTGCGAAGCGATCATCACGTCAGTCAGGTCGACGCCGCTCTTGCCGATTTCGAACGCGTTGGCCAGTTGGGTCGAGGCTTGCTGCGTCTCATGCACCTTGCCGATGGCCTGGCCGAGCATGTCGGCGAAGGTGCTTTGCCCTGGCGCCAGCTCGGGGGCGGCAGTTACCTTGGGCAGCGACATGGCATCGGCCTGCATGGCCCGCATGTCCAACATCAGACGATTGAATTCAACACCTTGGCTCATGACCCTTCTCTCTCCTGCGGCCGCATTTTTTT  >  NC_002947/4960562‑4960850

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.